Two-dimensional separation systems for protein samples are of great interest because of their increased peak capacity over one-dimensional systems. For example, separation of a complex protein mixture is currently performed using two-dimensional poly(acrylamide) gel electrophoresis, in which proteins are first separated by their iso-electric points, and then by size. The technique gives excellent separation of the protein mixture, but is very time consuming and labor intensive. Furthermore, because the proteins are embedded in the gel matrix, extensive protocols involving destaining, in-gel digestion, and extraction are necessary for further analysis by mass spectrometry, for example. Procedures that require considerable human intervention and a number of fluid transfers such as these can result in errors, contamination, and exposure to potential biohazards. Therefore, there remains a need for a device that is capable of providing limited user-intervention for two-dimensional separation and subsequent analysis.